Multiple sequence alignment - TraesCS1A01G292400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G292400 chr1A 100.000 3827 0 0 1 3827 488070523 488074349 0.000000e+00 7068.0
1 TraesCS1A01G292400 chr1A 82.060 1990 223 58 994 2955 488111937 488110054 0.000000e+00 1574.0
2 TraesCS1A01G292400 chr1A 85.308 422 42 11 3166 3570 488109452 488109034 5.910000e-113 418.0
3 TraesCS1A01G292400 chr1A 74.742 776 125 39 1015 1756 488103808 488103070 8.090000e-72 281.0
4 TraesCS1A01G292400 chr1A 73.576 825 133 53 993 1752 488235803 488236607 1.780000e-58 237.0
5 TraesCS1A01G292400 chr1A 92.771 83 4 2 3569 3650 488108984 488108903 6.720000e-23 119.0
6 TraesCS1A01G292400 chr1A 97.059 68 2 0 694 761 488071152 488071219 8.690000e-22 115.0
7 TraesCS1A01G292400 chr1A 97.059 68 2 0 630 697 488071216 488071283 8.690000e-22 115.0
8 TraesCS1A01G292400 chr1D 91.377 2818 156 35 807 3570 388990913 388993697 0.000000e+00 3777.0
9 TraesCS1A01G292400 chr1D 83.097 1621 175 50 924 2521 389213018 389214562 0.000000e+00 1384.0
10 TraesCS1A01G292400 chr1D 81.780 1663 198 51 1352 2975 389555636 389554040 0.000000e+00 1295.0
11 TraesCS1A01G292400 chr1D 82.785 1429 167 40 994 2410 389603021 389601660 0.000000e+00 1203.0
12 TraesCS1A01G292400 chr1D 92.857 700 32 10 1 697 388990209 388990893 0.000000e+00 1000.0
13 TraesCS1A01G292400 chr1D 86.288 423 37 11 3166 3570 389215713 389216132 1.260000e-119 440.0
14 TraesCS1A01G292400 chr1D 84.360 422 44 12 3166 3570 389599178 389598762 9.960000e-106 394.0
15 TraesCS1A01G292400 chr1D 95.349 215 8 2 3569 3782 388993725 388993938 1.320000e-89 340.0
16 TraesCS1A01G292400 chr1D 82.152 409 48 17 3182 3570 389553729 389553326 1.030000e-85 327.0
17 TraesCS1A01G292400 chr1D 81.622 370 59 6 921 1283 390402698 390402331 8.040000e-77 298.0
18 TraesCS1A01G292400 chr1D 74.282 801 137 42 993 1752 390409545 390408773 1.350000e-69 274.0
19 TraesCS1A01G292400 chr1D 89.062 128 12 1 3657 3782 389547048 389546921 1.420000e-34 158.0
20 TraesCS1A01G292400 chr1D 73.019 467 88 27 2523 2981 389245268 389245704 3.100000e-26 130.0
21 TraesCS1A01G292400 chr1D 92.045 88 5 2 3569 3655 389216182 389216268 5.190000e-24 122.0
22 TraesCS1A01G292400 chr1D 94.737 38 2 0 867 904 390727751 390727788 4.130000e-05 60.2
23 TraesCS1A01G292400 chr1B 93.312 2138 102 16 858 2981 522362723 522364833 0.000000e+00 3118.0
24 TraesCS1A01G292400 chr1B 83.011 1395 149 47 833 2212 522626350 522627671 0.000000e+00 1182.0
25 TraesCS1A01G292400 chr1B 94.351 655 28 8 1 653 522361830 522362477 0.000000e+00 996.0
26 TraesCS1A01G292400 chr1B 90.234 471 20 12 3337 3782 522365447 522365916 3.290000e-165 592.0
27 TraesCS1A01G292400 chr1B 94.983 299 13 2 2983 3280 522364883 522365180 5.790000e-128 468.0
28 TraesCS1A01G292400 chr1B 75.028 881 153 45 1002 1847 522840979 522840131 2.830000e-91 346.0
29 TraesCS1A01G292400 chr1B 81.951 410 48 12 3182 3570 522628868 522629272 1.330000e-84 324.0
30 TraesCS1A01G292400 chr1B 73.573 946 153 58 873 1752 523338158 523339072 4.870000e-69 272.0
31 TraesCS1A01G292400 chr1B 85.507 138 16 3 1346 1480 523237979 523238115 1.430000e-29 141.0
32 TraesCS1A01G292400 chr1B 75.731 342 42 25 873 1197 523207874 523208191 2.400000e-27 134.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G292400 chr1A 488070523 488074349 3826 False 2432.666667 7068 98.039333 1 3827 3 chr1A.!!$F2 3826
1 TraesCS1A01G292400 chr1A 488108903 488111937 3034 True 703.666667 1574 86.713000 994 3650 3 chr1A.!!$R2 2656
2 TraesCS1A01G292400 chr1A 488103070 488103808 738 True 281.000000 281 74.742000 1015 1756 1 chr1A.!!$R1 741
3 TraesCS1A01G292400 chr1A 488235803 488236607 804 False 237.000000 237 73.576000 993 1752 1 chr1A.!!$F1 759
4 TraesCS1A01G292400 chr1D 388990209 388993938 3729 False 1705.666667 3777 93.194333 1 3782 3 chr1D.!!$F3 3781
5 TraesCS1A01G292400 chr1D 389553326 389555636 2310 True 811.000000 1295 81.966000 1352 3570 2 chr1D.!!$R4 2218
6 TraesCS1A01G292400 chr1D 389598762 389603021 4259 True 798.500000 1203 83.572500 994 3570 2 chr1D.!!$R5 2576
7 TraesCS1A01G292400 chr1D 389213018 389216268 3250 False 648.666667 1384 87.143333 924 3655 3 chr1D.!!$F4 2731
8 TraesCS1A01G292400 chr1D 390408773 390409545 772 True 274.000000 274 74.282000 993 1752 1 chr1D.!!$R3 759
9 TraesCS1A01G292400 chr1B 522361830 522365916 4086 False 1293.500000 3118 93.220000 1 3782 4 chr1B.!!$F4 3781
10 TraesCS1A01G292400 chr1B 522626350 522629272 2922 False 753.000000 1182 82.481000 833 3570 2 chr1B.!!$F5 2737
11 TraesCS1A01G292400 chr1B 522840131 522840979 848 True 346.000000 346 75.028000 1002 1847 1 chr1B.!!$R1 845
12 TraesCS1A01G292400 chr1B 523338158 523339072 914 False 272.000000 272 73.573000 873 1752 1 chr1B.!!$F3 879

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
455 459 0.109551 AGTGACTGACAGTGCGATCG 60.110 55.0 14.14 11.69 0.00 3.69 F
456 460 0.109735 GTGACTGACAGTGCGATCGA 60.110 55.0 21.57 0.59 0.00 3.59 F
956 1063 0.179004 TCACGGCCACAAGGACAAAT 60.179 50.0 2.24 0.00 46.60 2.32 F
2040 2293 0.664166 CACATGGCGACCTTGTTTGC 60.664 55.0 12.51 0.00 39.41 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2281 1.193650 TCGATTTCGCAAACAAGGTCG 59.806 47.619 0.0 0.0 39.60 4.79 R
2044 2297 1.210478 CTCCCCCTTGTCAATGTCGAT 59.790 52.381 0.0 0.0 0.00 3.59 R
2387 2669 1.765314 GATATCAGCCACCCAGTCACT 59.235 52.381 0.0 0.0 0.00 3.41 R
3220 5571 0.107312 CAAGGTGAGAGGGCAGGATG 60.107 60.000 0.0 0.0 40.87 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 6.121776 TCCTAGAAAAACTGCTACATGGAA 57.878 37.500 0.00 0.00 0.00 3.53
97 99 4.776795 TGACTTGAGCAGTAATACACGA 57.223 40.909 0.00 0.00 35.01 4.35
106 108 9.589111 TTGAGCAGTAATACACGAATACATTTA 57.411 29.630 0.00 0.00 0.00 1.40
152 154 4.224715 CCTTTCCAGGTTTTCTCGAAAC 57.775 45.455 0.00 0.00 45.53 2.78
157 159 3.323979 TCCAGGTTTTCTCGAAACTAGCT 59.676 43.478 0.00 0.00 45.55 3.32
284 286 8.233868 CGATGATCTCAGAAAGAATATCGTACT 58.766 37.037 12.34 0.00 42.67 2.73
291 293 2.317679 AGAATATCGTACTCAGCGCG 57.682 50.000 0.00 0.00 0.00 6.86
354 356 8.061662 TTAGCTAGCTAATGTCGATCCTATCGA 61.062 40.741 29.22 7.86 44.33 3.59
395 398 5.522460 TGTAAACACTAGCTTCCGAATATGC 59.478 40.000 0.00 0.00 0.00 3.14
454 458 1.344458 CAGTGACTGACAGTGCGATC 58.656 55.000 14.14 0.00 41.99 3.69
455 459 0.109551 AGTGACTGACAGTGCGATCG 60.110 55.000 14.14 11.69 0.00 3.69
456 460 0.109735 GTGACTGACAGTGCGATCGA 60.110 55.000 21.57 0.59 0.00 3.59
457 461 0.811281 TGACTGACAGTGCGATCGAT 59.189 50.000 21.57 0.00 0.00 3.59
458 462 2.014128 TGACTGACAGTGCGATCGATA 58.986 47.619 21.57 3.49 0.00 2.92
540 544 4.489679 AAAGTCTGAAAATCTTCGCACC 57.510 40.909 0.00 0.00 33.94 5.01
597 604 8.552083 AATTCTTCTTGTTTGAGCTTGTTTTT 57.448 26.923 0.00 0.00 0.00 1.94
602 609 6.686630 TCTTGTTTGAGCTTGTTTTTCTCAA 58.313 32.000 0.00 0.00 42.88 3.02
674 681 6.127366 ACTGGCAAAAGTCTGAAAATCTGAAA 60.127 34.615 0.00 0.00 0.00 2.69
675 682 6.042143 TGGCAAAAGTCTGAAAATCTGAAAC 58.958 36.000 0.00 0.00 0.00 2.78
683 751 6.261826 AGTCTGAAAATCTGAAACAGGAGTTG 59.738 38.462 0.00 0.00 38.17 3.16
685 753 7.000472 TCTGAAAATCTGAAACAGGAGTTGAT 59.000 34.615 0.00 0.00 38.17 2.57
687 755 5.972107 AAATCTGAAACAGGAGTTGATGG 57.028 39.130 0.00 0.00 38.17 3.51
697 765 5.336102 ACAGGAGTTGATGGATTTTTGGAT 58.664 37.500 0.00 0.00 0.00 3.41
698 766 5.420104 ACAGGAGTTGATGGATTTTTGGATC 59.580 40.000 0.00 0.00 0.00 3.36
699 767 4.641989 AGGAGTTGATGGATTTTTGGATCG 59.358 41.667 0.00 0.00 0.00 3.69
702 770 3.781079 TGATGGATTTTTGGATCGTGC 57.219 42.857 0.00 0.00 0.00 5.34
703 771 2.426738 TGATGGATTTTTGGATCGTGCC 59.573 45.455 0.00 0.00 0.00 5.01
704 772 0.808125 TGGATTTTTGGATCGTGCCG 59.192 50.000 0.00 0.00 0.00 5.69
705 773 0.525455 GGATTTTTGGATCGTGCCGC 60.525 55.000 0.00 0.00 0.00 6.53
706 774 0.451783 GATTTTTGGATCGTGCCGCT 59.548 50.000 0.00 0.00 0.00 5.52
707 775 0.451783 ATTTTTGGATCGTGCCGCTC 59.548 50.000 0.00 0.00 0.00 5.03
708 776 1.906994 TTTTTGGATCGTGCCGCTCG 61.907 55.000 8.51 8.51 0.00 5.03
709 777 4.812476 TTGGATCGTGCCGCTCGG 62.812 66.667 14.32 3.56 38.57 4.63
739 807 6.275335 TGGCAAAAGTCTGAAAATCTGAAAG 58.725 36.000 0.00 0.00 0.00 2.62
764 832 6.552008 AGGAGTTGATGGATTTTTGGACTTA 58.448 36.000 0.00 0.00 0.00 2.24
786 854 5.986501 AGAAGTTCGAACTCACCTTATCT 57.013 39.130 29.82 22.49 38.57 1.98
787 855 5.956642 AGAAGTTCGAACTCACCTTATCTC 58.043 41.667 29.82 19.42 38.57 2.75
788 856 4.358494 AGTTCGAACTCACCTTATCTCG 57.642 45.455 24.93 0.00 32.86 4.04
789 857 3.757493 AGTTCGAACTCACCTTATCTCGT 59.243 43.478 24.93 0.00 32.86 4.18
790 858 4.940046 AGTTCGAACTCACCTTATCTCGTA 59.060 41.667 24.93 0.00 32.86 3.43
791 859 4.871993 TCGAACTCACCTTATCTCGTAC 57.128 45.455 0.00 0.00 0.00 3.67
792 860 3.624861 TCGAACTCACCTTATCTCGTACC 59.375 47.826 0.00 0.00 0.00 3.34
793 861 3.243002 CGAACTCACCTTATCTCGTACCC 60.243 52.174 0.00 0.00 0.00 3.69
794 862 2.664015 ACTCACCTTATCTCGTACCCC 58.336 52.381 0.00 0.00 0.00 4.95
795 863 2.244252 ACTCACCTTATCTCGTACCCCT 59.756 50.000 0.00 0.00 0.00 4.79
796 864 3.461085 ACTCACCTTATCTCGTACCCCTA 59.539 47.826 0.00 0.00 0.00 3.53
797 865 4.079558 ACTCACCTTATCTCGTACCCCTAA 60.080 45.833 0.00 0.00 0.00 2.69
798 866 4.870636 TCACCTTATCTCGTACCCCTAAA 58.129 43.478 0.00 0.00 0.00 1.85
799 867 5.271598 TCACCTTATCTCGTACCCCTAAAA 58.728 41.667 0.00 0.00 0.00 1.52
800 868 5.361857 TCACCTTATCTCGTACCCCTAAAAG 59.638 44.000 0.00 0.00 0.00 2.27
801 869 5.361857 CACCTTATCTCGTACCCCTAAAAGA 59.638 44.000 0.00 0.00 0.00 2.52
802 870 5.597594 ACCTTATCTCGTACCCCTAAAAGAG 59.402 44.000 0.00 0.00 0.00 2.85
803 871 5.832060 CCTTATCTCGTACCCCTAAAAGAGA 59.168 44.000 0.00 0.00 38.81 3.10
804 872 6.323225 CCTTATCTCGTACCCCTAAAAGAGAA 59.677 42.308 0.00 0.00 38.11 2.87
805 873 7.147776 CCTTATCTCGTACCCCTAAAAGAGAAA 60.148 40.741 0.00 0.00 38.11 2.52
817 885 9.734984 CCCCTAAAAGAGAAACTTATCTTTGTA 57.265 33.333 11.66 6.91 45.05 2.41
829 897 7.233389 ACTTATCTTTGTAGTCTTCTCTGCA 57.767 36.000 0.00 0.00 0.00 4.41
844 912 0.465097 CTGCAAGACCATGGGCTAGG 60.465 60.000 23.92 17.86 34.07 3.02
845 913 1.152881 GCAAGACCATGGGCTAGGG 60.153 63.158 23.92 15.06 35.97 3.53
847 915 1.507140 CAAGACCATGGGCTAGGGTA 58.493 55.000 23.92 0.00 45.06 3.69
848 916 1.417890 CAAGACCATGGGCTAGGGTAG 59.582 57.143 23.92 2.99 45.06 3.18
849 917 0.764752 AGACCATGGGCTAGGGTAGC 60.765 60.000 22.06 0.00 45.06 3.58
910 1017 0.555769 TGCACCAAACCCCTCTTTCT 59.444 50.000 0.00 0.00 0.00 2.52
916 1023 2.427506 CAAACCCCTCTTTCTCTTCCG 58.572 52.381 0.00 0.00 0.00 4.30
919 1026 1.605058 CCCCTCTTTCTCTTCCGCGA 61.605 60.000 8.23 0.00 0.00 5.87
956 1063 0.179004 TCACGGCCACAAGGACAAAT 60.179 50.000 2.24 0.00 46.60 2.32
969 1076 1.052287 GACAAATCTGCGCAAAACCG 58.948 50.000 13.05 0.00 0.00 4.44
971 1078 1.604755 ACAAATCTGCGCAAAACCGTA 59.395 42.857 13.05 0.00 0.00 4.02
987 1094 2.441532 TACCCCTCTTCGCCTCCG 60.442 66.667 0.00 0.00 0.00 4.63
1275 1443 2.697761 CCTCCTCGACTTCGCCGAA 61.698 63.158 0.00 0.00 39.60 4.30
1329 1497 1.377072 TGGCAGCAGCAAAGCGATA 60.377 52.632 2.65 0.00 44.61 2.92
1533 1755 3.847602 CAGCTCTGCCTCCGGGAG 61.848 72.222 17.41 17.41 42.73 4.30
1938 2190 5.765182 TGAGAAAAGATTGAACCTGGTCTTC 59.235 40.000 0.00 0.00 31.01 2.87
1959 2211 3.849574 TCCCTGACAAATCCATACCAAGA 59.150 43.478 0.00 0.00 0.00 3.02
2028 2281 6.091169 CCAACATTTTCTATTTCACACATGGC 59.909 38.462 0.00 0.00 0.00 4.40
2040 2293 0.664166 CACATGGCGACCTTGTTTGC 60.664 55.000 12.51 0.00 39.41 3.68
2044 2297 1.357334 GGCGACCTTGTTTGCGAAA 59.643 52.632 0.00 0.00 0.00 3.46
2055 2308 3.550561 TGTTTGCGAAATCGACATTGAC 58.449 40.909 7.06 5.03 43.02 3.18
2184 2440 5.266709 ACCTCCCGTGTACAGGTATATAT 57.733 43.478 14.08 0.00 38.86 0.86
2185 2441 6.392911 ACCTCCCGTGTACAGGTATATATA 57.607 41.667 14.08 0.00 38.86 0.86
2186 2442 6.978261 ACCTCCCGTGTACAGGTATATATAT 58.022 40.000 14.08 0.00 38.86 0.86
2187 2443 8.106017 ACCTCCCGTGTACAGGTATATATATA 57.894 38.462 14.08 0.00 38.86 0.86
2188 2444 8.730948 ACCTCCCGTGTACAGGTATATATATAT 58.269 37.037 14.08 10.10 38.86 0.86
2278 2534 3.791973 TGTTAGGGTGCACAAGTTTTG 57.208 42.857 20.43 0.00 0.00 2.44
2289 2571 6.200097 GGTGCACAAGTTTTGGTTTAACATAG 59.800 38.462 20.43 0.00 34.12 2.23
2315 2597 4.214310 TCAAATCATGTGTGTGGAACCTT 58.786 39.130 0.00 0.00 34.36 3.50
2316 2598 4.037803 TCAAATCATGTGTGTGGAACCTTG 59.962 41.667 0.00 0.00 34.36 3.61
2387 2669 4.899457 TCTGTACTGAAGTTTCTGAAGGGA 59.101 41.667 0.00 0.00 0.00 4.20
2392 2674 4.061596 CTGAAGTTTCTGAAGGGAGTGAC 58.938 47.826 0.00 0.00 0.00 3.67
2521 4279 3.181510 CGCAGGCAGAATTTTGTAGTACC 60.182 47.826 0.00 0.00 0.00 3.34
2561 4319 1.888512 GTTGAGTGCAATGGACATGGT 59.111 47.619 7.79 0.00 36.22 3.55
2708 4494 8.939201 AGATATACAGTTCTCATTGTTCTGTG 57.061 34.615 0.00 0.00 39.27 3.66
2780 4616 2.486966 GAGCAAGGCGACCAATGC 59.513 61.111 14.35 14.35 38.38 3.56
2822 4658 3.650139 ACATACTGGTTCGTGTTGACTC 58.350 45.455 0.00 0.00 0.00 3.36
2860 4696 3.940209 AAAAATCGAAGCATGCCAGAA 57.060 38.095 15.66 0.00 0.00 3.02
2884 4737 9.449719 GAATATCTTTGGTACTTCCTCTTGAAA 57.550 33.333 0.00 0.00 37.07 2.69
2904 4758 7.608308 TGAAAAATTCTTTCTTGTTTGGGTG 57.392 32.000 11.68 0.00 0.00 4.61
2921 4775 1.134367 GGTGCCCTTCTTATTTTCGCC 59.866 52.381 0.00 0.00 0.00 5.54
3013 4921 1.956477 AGTTTGGTCAAGTCACCATGC 59.044 47.619 0.00 0.00 46.21 4.06
3033 5178 3.198200 TGCCGAACTGCTACCCTAATTTA 59.802 43.478 0.00 0.00 0.00 1.40
3138 5438 6.599356 TCAGTGCTTTGTACAGGAGTATTA 57.401 37.500 0.00 0.00 31.84 0.98
3229 5580 1.064389 AGCCTAAAAGTCATCCTGCCC 60.064 52.381 0.00 0.00 0.00 5.36
3280 5662 8.397575 TCACTAGTCACTAATCCTGATATGTC 57.602 38.462 0.00 0.00 0.00 3.06
3319 5864 6.058183 ACTGAACTGAAGTATGTTTCTTGCT 58.942 36.000 0.00 0.00 0.00 3.91
3320 5865 7.217200 ACTGAACTGAAGTATGTTTCTTGCTA 58.783 34.615 0.00 0.00 0.00 3.49
3321 5866 7.386299 ACTGAACTGAAGTATGTTTCTTGCTAG 59.614 37.037 0.00 0.00 0.00 3.42
3322 5867 6.147821 TGAACTGAAGTATGTTTCTTGCTAGC 59.852 38.462 8.10 8.10 0.00 3.42
3641 6295 1.797635 GATGCTTATCTTCTCCGCAGC 59.202 52.381 0.00 0.00 33.72 5.25
3686 6340 8.746052 AGGATATGTTTGATCGGATTGTTTTA 57.254 30.769 0.00 0.00 0.00 1.52
3708 6363 2.031683 GTGCATAGGTCATTTACGTGGC 59.968 50.000 0.00 0.00 0.00 5.01
3793 6448 5.873179 TTCCAGTGGAAAACGATATGTTC 57.127 39.130 22.59 0.00 40.84 3.18
3794 6449 4.258543 TCCAGTGGAAAACGATATGTTCC 58.741 43.478 10.20 0.00 40.84 3.62
3795 6450 3.377172 CCAGTGGAAAACGATATGTTCCC 59.623 47.826 1.68 0.00 40.84 3.97
3796 6451 4.261801 CAGTGGAAAACGATATGTTCCCT 58.738 43.478 0.00 0.00 40.84 4.20
3797 6452 4.094887 CAGTGGAAAACGATATGTTCCCTG 59.905 45.833 0.00 0.00 40.84 4.45
3798 6453 4.007659 GTGGAAAACGATATGTTCCCTGT 58.992 43.478 0.00 0.00 40.84 4.00
3799 6454 4.457949 GTGGAAAACGATATGTTCCCTGTT 59.542 41.667 0.00 0.00 40.84 3.16
3800 6455 4.698304 TGGAAAACGATATGTTCCCTGTTC 59.302 41.667 0.00 0.00 40.84 3.18
3801 6456 4.941873 GGAAAACGATATGTTCCCTGTTCT 59.058 41.667 0.00 0.00 40.84 3.01
3802 6457 6.110707 GGAAAACGATATGTTCCCTGTTCTA 58.889 40.000 0.00 0.00 40.84 2.10
3803 6458 6.596497 GGAAAACGATATGTTCCCTGTTCTAA 59.404 38.462 0.00 0.00 40.84 2.10
3804 6459 7.120138 GGAAAACGATATGTTCCCTGTTCTAAA 59.880 37.037 0.00 0.00 40.84 1.85
3805 6460 8.575649 AAAACGATATGTTCCCTGTTCTAAAT 57.424 30.769 0.00 0.00 40.84 1.40
3806 6461 7.553881 AACGATATGTTCCCTGTTCTAAATG 57.446 36.000 0.00 0.00 35.27 2.32
3807 6462 6.650120 ACGATATGTTCCCTGTTCTAAATGT 58.350 36.000 0.00 0.00 0.00 2.71
3808 6463 7.110155 ACGATATGTTCCCTGTTCTAAATGTT 58.890 34.615 0.00 0.00 0.00 2.71
3809 6464 8.262227 ACGATATGTTCCCTGTTCTAAATGTTA 58.738 33.333 0.00 0.00 0.00 2.41
3810 6465 9.273016 CGATATGTTCCCTGTTCTAAATGTTAT 57.727 33.333 0.00 0.00 0.00 1.89
3814 6469 9.927668 ATGTTCCCTGTTCTAAATGTTATTTTG 57.072 29.630 0.00 0.00 0.00 2.44
3815 6470 8.364142 TGTTCCCTGTTCTAAATGTTATTTTGG 58.636 33.333 0.00 0.00 0.00 3.28
3816 6471 8.364894 GTTCCCTGTTCTAAATGTTATTTTGGT 58.635 33.333 0.00 0.00 0.00 3.67
3817 6472 8.117813 TCCCTGTTCTAAATGTTATTTTGGTC 57.882 34.615 0.00 0.00 0.00 4.02
3818 6473 7.947890 TCCCTGTTCTAAATGTTATTTTGGTCT 59.052 33.333 0.00 0.00 0.00 3.85
3819 6474 8.585018 CCCTGTTCTAAATGTTATTTTGGTCTT 58.415 33.333 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.164230 TCTAGGAAGAGAAACAGAATCTCAC 57.836 40.000 6.35 0.69 44.64 3.51
56 58 1.975660 TGTCGGTAAAGCAAGCCTTT 58.024 45.000 0.00 0.00 45.44 3.11
106 108 8.141909 GGTGGAAGCAAAGTTTTAGTAAGAAAT 58.858 33.333 0.00 0.00 0.00 2.17
109 111 6.362248 AGGTGGAAGCAAAGTTTTAGTAAGA 58.638 36.000 0.00 0.00 36.26 2.10
116 118 3.517500 TGGAAAGGTGGAAGCAAAGTTTT 59.482 39.130 0.00 0.00 36.26 2.43
121 123 1.063266 ACCTGGAAAGGTGGAAGCAAA 60.063 47.619 0.00 0.00 41.33 3.68
284 286 1.807142 CTAGAGATACATCCGCGCTGA 59.193 52.381 5.56 4.40 0.00 4.26
291 293 9.444600 CCTTAGTAGAGAACTAGAGATACATCC 57.555 40.741 0.00 0.00 41.70 3.51
354 356 0.106519 ACAGGCAAGCTGTGGAGTTT 60.107 50.000 0.00 0.00 33.29 2.66
395 398 1.611491 AGGGCATTTACAAACCACACG 59.389 47.619 0.00 0.00 0.00 4.49
597 604 5.434182 TCAACATACATGACCCATTGAGA 57.566 39.130 0.00 0.00 0.00 3.27
602 609 6.406177 GCAAAGAATCAACATACATGACCCAT 60.406 38.462 0.00 0.00 0.00 4.00
655 662 7.340487 ACTCCTGTTTCAGATTTTCAGACTTTT 59.660 33.333 0.00 0.00 32.44 2.27
674 681 4.739793 TCCAAAAATCCATCAACTCCTGT 58.260 39.130 0.00 0.00 0.00 4.00
675 682 5.449588 CGATCCAAAAATCCATCAACTCCTG 60.450 44.000 0.00 0.00 0.00 3.86
683 751 3.084070 GGCACGATCCAAAAATCCATC 57.916 47.619 0.00 0.00 0.00 3.51
710 778 5.474876 AGATTTTCAGACTTTTGCCAGTAGG 59.525 40.000 0.00 0.00 38.23 3.18
711 779 6.205464 TCAGATTTTCAGACTTTTGCCAGTAG 59.795 38.462 0.00 0.00 0.00 2.57
712 780 6.061441 TCAGATTTTCAGACTTTTGCCAGTA 58.939 36.000 0.00 0.00 0.00 2.74
713 781 4.889409 TCAGATTTTCAGACTTTTGCCAGT 59.111 37.500 0.00 0.00 0.00 4.00
714 782 5.443185 TCAGATTTTCAGACTTTTGCCAG 57.557 39.130 0.00 0.00 0.00 4.85
715 783 5.850557 TTCAGATTTTCAGACTTTTGCCA 57.149 34.783 0.00 0.00 0.00 4.92
716 784 6.507023 TCTTTCAGATTTTCAGACTTTTGCC 58.493 36.000 0.00 0.00 0.00 4.52
717 785 6.640092 CCTCTTTCAGATTTTCAGACTTTTGC 59.360 38.462 0.00 0.00 0.00 3.68
718 786 7.934457 TCCTCTTTCAGATTTTCAGACTTTTG 58.066 34.615 0.00 0.00 0.00 2.44
719 787 7.777440 ACTCCTCTTTCAGATTTTCAGACTTTT 59.223 33.333 0.00 0.00 0.00 2.27
720 788 7.286313 ACTCCTCTTTCAGATTTTCAGACTTT 58.714 34.615 0.00 0.00 0.00 2.66
721 789 6.836242 ACTCCTCTTTCAGATTTTCAGACTT 58.164 36.000 0.00 0.00 0.00 3.01
722 790 6.432403 ACTCCTCTTTCAGATTTTCAGACT 57.568 37.500 0.00 0.00 0.00 3.24
723 791 6.708054 TCAACTCCTCTTTCAGATTTTCAGAC 59.292 38.462 0.00 0.00 0.00 3.51
724 792 6.830912 TCAACTCCTCTTTCAGATTTTCAGA 58.169 36.000 0.00 0.00 0.00 3.27
725 793 7.361885 CCATCAACTCCTCTTTCAGATTTTCAG 60.362 40.741 0.00 0.00 0.00 3.02
726 794 6.432162 CCATCAACTCCTCTTTCAGATTTTCA 59.568 38.462 0.00 0.00 0.00 2.69
727 795 6.656693 TCCATCAACTCCTCTTTCAGATTTTC 59.343 38.462 0.00 0.00 0.00 2.29
739 807 5.012893 AGTCCAAAAATCCATCAACTCCTC 58.987 41.667 0.00 0.00 0.00 3.71
747 815 7.119262 TCGAACTTCTAAGTCCAAAAATCCATC 59.881 37.037 0.00 0.00 38.57 3.51
751 819 7.862648 AGTTCGAACTTCTAAGTCCAAAAATC 58.137 34.615 24.93 0.00 38.57 2.17
764 832 5.392165 CGAGATAAGGTGAGTTCGAACTTCT 60.392 44.000 30.22 24.89 39.88 2.85
786 854 5.813513 AAGTTTCTCTTTTAGGGGTACGA 57.186 39.130 0.00 0.00 31.57 3.43
787 855 7.554211 AGATAAGTTTCTCTTTTAGGGGTACG 58.446 38.462 0.00 0.00 37.56 3.67
788 856 9.736414 AAAGATAAGTTTCTCTTTTAGGGGTAC 57.264 33.333 7.11 0.00 38.27 3.34
789 857 9.734984 CAAAGATAAGTTTCTCTTTTAGGGGTA 57.265 33.333 9.31 0.00 39.15 3.69
790 858 8.225416 ACAAAGATAAGTTTCTCTTTTAGGGGT 58.775 33.333 9.31 3.93 39.15 4.95
791 859 8.637196 ACAAAGATAAGTTTCTCTTTTAGGGG 57.363 34.615 9.31 3.48 39.15 4.79
801 869 9.921637 CAGAGAAGACTACAAAGATAAGTTTCT 57.078 33.333 0.00 0.00 0.00 2.52
802 870 8.652463 GCAGAGAAGACTACAAAGATAAGTTTC 58.348 37.037 0.00 0.00 0.00 2.78
803 871 8.150945 TGCAGAGAAGACTACAAAGATAAGTTT 58.849 33.333 0.00 0.00 0.00 2.66
804 872 7.671302 TGCAGAGAAGACTACAAAGATAAGTT 58.329 34.615 0.00 0.00 0.00 2.66
805 873 7.233389 TGCAGAGAAGACTACAAAGATAAGT 57.767 36.000 0.00 0.00 0.00 2.24
829 897 1.807814 CTACCCTAGCCCATGGTCTT 58.192 55.000 11.73 0.00 33.55 3.01
853 921 2.281970 CTCTGGCTGGCACAAGCA 60.282 61.111 0.00 0.00 44.61 3.91
910 1017 0.108804 GATCTGTGGTTCGCGGAAGA 60.109 55.000 6.13 0.00 32.81 2.87
919 1026 0.388649 GACGTGAGCGATCTGTGGTT 60.389 55.000 0.90 0.00 42.00 3.67
946 1053 2.420628 TTTGCGCAGATTTGTCCTTG 57.579 45.000 11.31 0.00 0.00 3.61
956 1063 1.962306 GGGTACGGTTTTGCGCAGA 60.962 57.895 11.31 2.14 0.00 4.26
969 1076 2.783288 CGGAGGCGAAGAGGGGTAC 61.783 68.421 0.00 0.00 0.00 3.34
1533 1755 3.623703 GACCCTTTGGCCGTCCCTC 62.624 68.421 0.00 0.00 33.59 4.30
1896 2148 3.055819 TCTCATGTGTTAGCTTCCAGGAC 60.056 47.826 0.00 0.00 0.00 3.85
1938 2190 4.080356 TCTCTTGGTATGGATTTGTCAGGG 60.080 45.833 0.00 0.00 0.00 4.45
1959 2211 2.198827 TCCACGGCATTTCACATTCT 57.801 45.000 0.00 0.00 0.00 2.40
2028 2281 1.193650 TCGATTTCGCAAACAAGGTCG 59.806 47.619 0.00 0.00 39.60 4.79
2040 2293 2.095853 CCCCTTGTCAATGTCGATTTCG 59.904 50.000 0.00 0.00 41.45 3.46
2044 2297 1.210478 CTCCCCCTTGTCAATGTCGAT 59.790 52.381 0.00 0.00 0.00 3.59
2055 2308 1.997874 CCTCCCAGTCTCCCCCTTG 60.998 68.421 0.00 0.00 0.00 3.61
2187 2443 9.736414 AAGAATGCATGTCTAAGAAGCATATAT 57.264 29.630 0.00 0.00 44.40 0.86
2188 2444 8.996271 CAAGAATGCATGTCTAAGAAGCATATA 58.004 33.333 0.00 0.00 44.40 0.86
2189 2445 7.718314 TCAAGAATGCATGTCTAAGAAGCATAT 59.282 33.333 0.00 0.00 44.40 1.78
2289 2571 5.234116 GGTTCCACACACATGATTTGAAAAC 59.766 40.000 0.00 0.00 0.00 2.43
2349 2631 7.889589 TCAGTACAGATACAATTTGTGTCAG 57.110 36.000 23.02 18.68 40.39 3.51
2387 2669 1.765314 GATATCAGCCACCCAGTCACT 59.235 52.381 0.00 0.00 0.00 3.41
2392 2674 5.380043 ACATTTAAGATATCAGCCACCCAG 58.620 41.667 5.32 0.00 0.00 4.45
2521 4279 7.173907 ACTCAACAAAATACACCAGATTCTCTG 59.826 37.037 0.00 0.00 43.91 3.35
2546 4304 5.772825 ATACAATACCATGTCCATTGCAC 57.227 39.130 9.75 0.00 33.82 4.57
2704 4490 9.086336 ACAAGAAATTAAACACAAATGACACAG 57.914 29.630 0.00 0.00 0.00 3.66
2780 4616 2.951642 TCTGCCAAAGTCTTCCTTGTTG 59.048 45.455 0.00 0.00 32.32 3.33
2853 4689 5.191722 AGGAAGTACCAAAGATATTCTGGCA 59.808 40.000 0.00 0.00 42.04 4.92
2859 4695 9.807921 TTTTCAAGAGGAAGTACCAAAGATATT 57.192 29.630 0.00 0.00 42.04 1.28
2860 4696 9.807921 TTTTTCAAGAGGAAGTACCAAAGATAT 57.192 29.630 0.00 0.00 42.04 1.63
2884 4737 4.450976 GGCACCCAAACAAGAAAGAATTT 58.549 39.130 0.00 0.00 43.98 1.82
2904 4758 2.365582 TCAGGCGAAAATAAGAAGGGC 58.634 47.619 0.00 0.00 0.00 5.19
2981 4837 5.601313 ACTTGACCAAACTACTTACTCCTGA 59.399 40.000 0.00 0.00 0.00 3.86
3013 4921 3.800506 CGTAAATTAGGGTAGCAGTTCGG 59.199 47.826 0.00 0.00 0.00 4.30
3138 5438 6.264292 CAGCATGGTAGTAGAGTAGTTCAGAT 59.736 42.308 0.00 0.00 0.00 2.90
3205 5556 4.021104 GGCAGGATGACTTTTAGGCTTTTT 60.021 41.667 0.00 0.00 44.72 1.94
3220 5571 0.107312 CAAGGTGAGAGGGCAGGATG 60.107 60.000 0.00 0.00 40.87 3.51
3229 5580 6.347696 AGAATAAAGCTGATCAAGGTGAGAG 58.652 40.000 0.00 0.00 36.51 3.20
3280 5662 7.439157 TCAGTTCAGTCTTGATTTGGTAATG 57.561 36.000 0.00 0.00 32.27 1.90
3424 6003 8.791605 CAAAAGAGTAAACGGTAAAACAGAAAC 58.208 33.333 0.00 0.00 0.00 2.78
3532 6112 1.234615 AACACGCCAAGATTGTCCCG 61.235 55.000 0.00 0.00 0.00 5.14
3581 6234 3.253188 GTGCATTTGTTAGACTGCTCCAA 59.747 43.478 0.00 0.00 35.66 3.53
3641 6295 6.698008 TCCTTTGATAGGTGCAATAACATG 57.302 37.500 0.00 0.00 45.03 3.21
3676 6330 6.699575 ATGACCTATGCACTAAAACAATCC 57.300 37.500 0.00 0.00 0.00 3.01
3686 6340 3.531538 CCACGTAAATGACCTATGCACT 58.468 45.455 0.00 0.00 0.00 4.40
3708 6363 5.164090 GCGCATGCATTTCTTATCATCATTG 60.164 40.000 19.57 0.00 42.15 2.82
3782 6437 7.110155 ACATTTAGAACAGGGAACATATCGTT 58.890 34.615 0.00 0.00 41.86 3.85
3783 6438 6.650120 ACATTTAGAACAGGGAACATATCGT 58.350 36.000 0.00 0.00 0.00 3.73
3784 6439 7.553881 AACATTTAGAACAGGGAACATATCG 57.446 36.000 0.00 0.00 0.00 2.92
3788 6443 9.927668 CAAAATAACATTTAGAACAGGGAACAT 57.072 29.630 0.00 0.00 0.00 2.71
3789 6444 8.364142 CCAAAATAACATTTAGAACAGGGAACA 58.636 33.333 0.00 0.00 0.00 3.18
3790 6445 8.364894 ACCAAAATAACATTTAGAACAGGGAAC 58.635 33.333 0.00 0.00 0.00 3.62
3791 6446 8.485578 ACCAAAATAACATTTAGAACAGGGAA 57.514 30.769 0.00 0.00 0.00 3.97
3792 6447 7.947890 AGACCAAAATAACATTTAGAACAGGGA 59.052 33.333 0.00 0.00 0.00 4.20
3793 6448 8.122472 AGACCAAAATAACATTTAGAACAGGG 57.878 34.615 0.00 0.00 0.00 4.45


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.